Genomics and Applied Biology 2024, Vol.15, No.1, 54-63 http://bioscipublisher.com/index.php/gab 55 In addition to exploring genomic diversity, this study will analyze the evolutionary mechanisms that have shaped the Oryza genus. By comparing the genomes of different Oryza species, we aim to identify specific genetic changes associated with adaptation, speciation, and domestication. The research will highlight the role of natural selection, gene duplication, and structural variations in driving the evolutionary processes within the genus. Understanding these mechanisms will provide insights into the evolutionary history of rice and inform strategies for utilizing wild genetic resources in rice improvement programs. 1 Literature Review 1.1 Classification and distribution of Oryza genus The genus Oryza comprises approximately 24 species, including two cultivated species, Oryza sativa and Oryza glaberrima, and 22 wild species. These species are distributed across various geographical regions and ecological environments, reflecting a wide range of adaptations (Figure 1) (Stein et al., 2018). The genus is divided into ten distinct genome types, six diploid and four polyploid, with genome sizes varying significantly from 357 Mbp in Oryza glaberrima to 1283 Mbp in the polyploid Oryza ridleyi. The wild species of Oryza are particularly valuable as they harbor a reservoir of agriculturally important genes that can be utilized for crop improvemen. Figure 1 Geographic distribution and phylogenetic reconstruction of wild species of Oryza and Leersia (Adopted from Stein et al., 2018) Image Caption: a, Geographic ranges of wild Oryza species and the outgroup species L. perrieri sequenced in this study. Dashed red lines show the limits of rice cultivation. Mapped ranges are adapted from IRRI’s Knowledge Bank (see URLs). b, Most frequently estimated species phylogeny in supermatrix and MP-EST analyses of each chromosome (inferred in 10 of 12 chromosomes and 11 of 12 chromosomes, respectively). Bootstrap proportions were obtained from 400 supermatrix bootstrap replicates, and MP-EST support values were obtained as described in the Methods. All clades were supported by both methods at 100%, except as indicated. Divergence times within the Oryza genus were estimated by PATHd8, assuming an age of 15 million years for the Oryza crown group. Bars on nodes represent the range of PATHd8 age estimates across all 12 chromosomes. Mya, million years ago (Adopted from Stein et al., 2018) Stein et al. (2018) provides insights into the evolutionary timeline and biogeography of rice species, which is crucial for understanding genetic diversity and guiding rice breeding programs to enhance crop resilience and productivity. The figure presents a study on the evolutionary history and geographic distribution of Oryza species, the genus to which rice belongs. Panel (a) maps the distribution of various Oryza species and Leersia perrieri across the globe, highlighting distinct geographic regions for each species. For instance, O. glumaepatula is found in South America, while O. nivara and O. rufipogon are primarily located in Asia. Figure 1Panel (b) depicts a
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